香猪基因组外显子SNPs检测及繁殖和体型性状候选基因分析

doi:10.16431/j.cnki.1671-7236.2021.02.016

Abstract

Abstract: In order to explore the molecular mechanism of early sexual maturity,low litter size and small body size of Xiang pig at the genomic level,we downloaded the re-sequencing data of Meishan pig and Duroc pig,which had obviously differences in reproduction and body-size as references.SNPs detection and allele frequency difference analysis were carried out on the re-sequencing data of 26 Xiang pigs,24 Meishan pigs and 24 Duroc pigs.The SNPs highly differentiated from Meishan pig and Duroc pig were detected by AS-PCR and Sanger sequencing.Finally,GO enrichment and KEGG pathway analysis were performed for genes with highly differentiated SNPs.The results showed that there were 236 710 SNPs in exons of Xiang pig genome,including 193 of stoplosses,1 238 of stopgains,90 945 of nonsynonymous SNPs and 144 334 synonymous SNPs.A total of 1 046 highly differentiated SNPs were obtained,including 429 of nonsynonymous SNPs,2 of stoplosses,6 of stopgains and 609 of synonymous SNPs,which affected 524 protein coding genes,and a hotspot rich in highly differentiated SNPs in 44-58 Mb of X chromosome was found.The results of allele frequency verification in populations were consistent with the re-sequencing results.8 loci were identified as highly differentiated SNPs in Xiang pig from Meishan pig and Duroc pig.Analysis for the 524 affected genes through GO and KEGG classification,it enriched in the oocyte meiosis,estrogen signaling pathway,estrogen signaling pathway together with other reproduction-related pathways.GO terms were annotated to intracellular estrogen receptor signaling,cilia movement and other reproduction-related items,skeletal system morphogenesis,bone development,osteoblast differentiation and other body-related items.The 18 reproduction-related genes PTGFR,TRO,DNAH17,PKDREJ,KAT8,DNAI2,VDR,TEX14,QSOX1,AR,WNK3,ADCY3,SPEF1,MIGA2,SLC2A8,PSMF1,TBC1D20,IFT172 and 7 size-related genes IBSP,NR6A1,HSPG2,TARS,PDZD2,FGF4,AMER1 with highly differentiated SNPs of Xiang pigs were identified,which might be the key genes to regulate the early sexual maturity,small litter size and small body size of Xiang pigs.

Key words: SNPs; Xiang pig; reproduction; body type; candidate genes

CLC Number:

S828

SUN Lingzhu, RAN Xueqin, LIU Chang, NIU Xi, HUANG Shihui, WANG Jiafu. Detection of Genome Exon SNPs and Analysis of Candidate Genes for Reproduction and Body Type Traits in Xiang Pig[J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(2): 537-553.

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Detection of Genome Exon SNPs and Analysis of Candidate Genes for Reproduction and Body Type Traits in Xiang Pig

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